diff --git a/biology/py-scikit-bio/Makefile b/biology/py-scikit-bio/Makefile
index 03efdcfe9af3..4297e08f2c1c 100644
--- a/biology/py-scikit-bio/Makefile
+++ b/biology/py-scikit-bio/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	scikit-bio
-DISTVERSION=	0.6.2
+DISTVERSION=	0.6.3
 CATEGORIES=	biology education python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -34,10 +34,9 @@ RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}biom-format>0:biology/py-biom-format@${PY_FL
 		${PYTHON_PKGNAMEPREFIX}statsmodels>=0.14.0:math/py-statsmodels@${PY_FLAVOR}
 
 USES=		python
-USE_PYTHON=	pep517 cython autoplist pytest # tests fail to run, see https://github.com/biocore/scikit-bio/issues/1846
+USE_PYTHON=	pep517 cython autoplist pytest
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
-TEST_WRKSRC=	${WRKSRC}/skbio/tests
 
 CONFLICTS_INSTALL=	${PYTHON_PKGNAMEPREFIX}ddtrace # lib/python3.8/site-packages/benchmarks/__init__.py
 
@@ -53,4 +52,10 @@ post-install:
 		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*${PYTHON_EXT_SUFFIX}.so \
 		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*/*${PYTHON_EXT_SUFFIX}.so
 
+do-test: # tests fail to run in a regular way, see https://github.com/biocore/scikit-bio/issues/1846
+	@cd ${STAGEDIR}${PYTHON_SITELIBDIR} && \
+		${SETENV} ${TEST_ENV} pytest .
+
+# tests as of 0.6.3: 2792 passed, 30 skipped, 56 warnings in 250.28s (0:04:10)
+
 .include <bsd.port.mk>
diff --git a/biology/py-scikit-bio/distinfo b/biology/py-scikit-bio/distinfo
index fa11401cb467..370eba0445bd 100644
--- a/biology/py-scikit-bio/distinfo
+++ b/biology/py-scikit-bio/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1720838021
-SHA256 (scikit-bio-0.6.2.tar.gz) = af217ad12243cdaeef74a8f3bebe0d04aefda2a22d963d634201a36318b1a404
-SIZE (scikit-bio-0.6.2.tar.gz) = 2699488
+TIMESTAMP = 1736808587
+SHA256 (scikit-bio-0.6.3.tar.gz) = f06cc87a1823902906821819e66f7cd704563a9f8cdf6720296a42dcbc2fe1c2
+SIZE (scikit-bio-0.6.3.tar.gz) = 5356619